High power GaN-based LEDs with nano-structured Ga-doped ZnO (GZO) transparent conductive layer (TCL) were fabricated by using metal-organic chemical vapor deposition (MOCVD) method. Compared with the conventional LED with Ni/Au or ITO process, the saturation current in the LEDs with GZO TCL approximately increased up to more than 14 % and 13 %, and the light output intensity up to 57.5 % and 30.1 %, respectively. This improvement was attributed to the high carrier concentration of GZO TCL and the planar structure at the TCL bottom, which improved the electrical conductivity, and therefore promoted current spreading. The refractive index of GZO is similar to GaN (n ≈ 2) and thereby results in the reduction of the reflection loss between GaN and TCL interface. In addition, the nano-structure of GZO TCL increased the light output critical angle and enhanced surface light emitting while reducing the lateral light loss and consequently improved light extraction efficiency of LEDs.